MolNFT v2 · #116988 · protein + DNA
Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Methylhymidine
5DLG: “Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Methylhymidine”. X-ray diffraction at 2.351, 2 ligands (XG4, MG), 3 pockets (best druggability 0.84). MolNFT v2 #116988 on GenesisL1: 3D structure, binding…
- PDB
- 5DLG
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.351
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase eta; DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- XG4, MG
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.351 · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 430 | 44% helix, 22% strand | Q9Y253 |
| P | DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3') | dna | 8 | — | — |
| T | DNA (5'-D(*CP*AP*TP*(5DB)P*AP*TP*GP*AP*CP*GP*CP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A, P
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.84 | 0.85 | 85 | XG4 |
| 2 | 232 | 0.63 | 0.82 | 26 | empty |
| 3 | 93 | 0.38 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1026 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–P · 597 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–T · 373 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5DLG · Crystal structure of human DNA polymerase eta inserting dgmpnpp opposite O4-methylhymidine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y253 · AlphaFold monomer V2.0 prediction for DNA polymerase eta (Q9Y253) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9Y253
- Elsewhere: RCSB PDB 5DLG · PDBe 5DLG · UniProt Q9Y253
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